The field of antisense therapy involves techniques that attempt to treat a variety of disorders that are associated with genetic deficiencies or defects. One type of gene therapy treatment takes the form of treating the patient with a regulatory molecule, such as an antisense DNA oligodeoxyribonucleotide (ODN) molecule that binds to messenger RNA (mRNA) with the subsequent inhibition or control of translation and, hence, control of the production of a protein product. The antisense molecule is typically an oligonucleotide modified so as to have a long lifetime in the presence of cellular nucleases as well as to have high efficiency in hybridization to the target mRNA or genomic DNA. However, these modifications can result in undesirable side effects, one of which is that the ODN binds to cellular proteins and inhibits cellular functions in unpredictable ways [Mercola & Cohen, 1995; Orr & Monia 1998; Eckstein 2000]1. FIG. 1 illustrates the fact that the desired effect of an antisense ODN requires that the ODN reach the target mRNA in the cellular nucleus and that the ODN be able to selectively bind to a region (typically 20 nucleotides long) of the target mRNA, but not to other mRNAs. Non-specific binding to cellular proteins on the cell surface, in the cytoplasm, or in other compartments, including the nucleus, can reduce effective ODN concentrations. Therefore, the antisense effect in vivo is dependent on many factors.
1 All of the references cited herein and provided in the disclosed Bibliography are fully incorporated by reference in the specification. 
Antisense oligodeoxyribonucleotides (ODNs), typically designed to be complementary to a specific mRNA target sequence of about 20 nucleotides, have been shown to be effective as a means of transient disruption of gene expression at the translational level [Sokol et al., 1998; Sokol & Gewirtz, 1999]. Thirteen antisense ODNs, six of which are targeted to cancer genes, are approved or are in clinical trials [Braasch & Corey, 2002]. The first generation of antisense drugs consists of phosphorothioate-modified oligodeoxyribonucleotides (S-ODNs), in which one of the non-bridging oxygens is replaced by sulfur to inhibit nuclease degradation. S-ODNs, like unmodified DNA, exert their effect mainly by activating RNAse H, which binds to the sites of S-ODN:mRNA hybridization and cleaves the mRNA. There is growing evidence that this antisense effect takes place in the nucleus, although the uptake mechanism and nuclear localization can depend on ODN concentration [Beltinger et al., 1995; Gray et al., 1997; Orr & Monia, 1998; Sokol & Gewirtz, 1999]. Methods are now available to correlate ODN:mRNA hybridization with a reduction in mRNA and protein levels [Sokol et al., 1998; Sokol & Gewitz, 1999].
S-ODNs can exert a true antisense inhibition of translation, which is sequence-specific, as exemplified in studies of C-raf and A-raf inhibition by S-ODNs with increasing numbers of mismatches [Coiffi et al., 1997]. However, a plethora of effects, broadly denoted as non-specific, compromise the ability to predict true sequence-specific antisense effects on the basis of in vitro hybridization data [Branch, 1998; Stein, 1999]. These non-specific effects include the competing secondary structures of mRNA target sites, partial complementarity of ODNs with unintended sites, the interactions of ODNs with intracellular and extracellular proteins, ODN self-structures such as G-quartet structures (although G-containing tetraplex structures may not form under intracellular conditions [Basu & Wickstrom, 1997]), effects of carriers, the cell type, the particular mRNA that is targeted, and conditions at the mRNA target site. Moreover, cellular delivery and subcellular trafficking may be somewhat sequence specific [Stein & Cheng, 1993; Wagner & Flanagan, 1997]. The type of ODN modification is also important. Chemical modifications other than phosphorothioate modification, such as 2′-O-alkyl and 2′-O-methoxyethoxy modifications, methylphosphonation, and 2′-5′ linkage of 3′-deoxyribonucleotides, have been used to increase the stability and reduce the non-specific effects of antisense S-ODNs [Monia et al., 1993; Gray et al., 1997; Giles et al., 1998]. However, these modifications reduce RNase H sensitivity. For this reason, chimeric antisense ODNs that combine such modifications together with five to seven simple phosphorothioate nucleotides (to retain RNase H sensitivity) have been advocated [Monia et al., 1993]. Phosphorothioate modification thus remains an important modification.
Non-specific effects are not necessarily bad if they offer an added source of drug potency [Branch, 1998]. However, non-specific effects of ODN sequences have been difficult to predict, and a bottleneck remaining in the design of antisense drugs is the inability to make rational, a priori, selections of the best mRNA target sequences [Branch, 1998; Bernstein, 1998; Eckstein, 1998]. Others in the field are moving toward streamlined testing of all possible accessible sites on a target mRNA [Eckstein, 1998; Ho et al., 1998; Matveeva et al., 1998].